National pride should not be underestimated (the US felt proprietary about the bomb and was not going to give another nation undue credit for it), but here are a few other ways to think about it:

• It was not a matter of just picking a plane and then dropping a bomb. The planes had to be heavily modified to carry the Fat Man bomb (the B-29 was through the Silverplate program, and a Lancaster would have had to have been as well), but also had crews that had practiced flying the distances, dropping similar bomb shapes, and so on (part of Project Alberta). The US Army was going to run all of that — integrating a non-US plane (and non-US crew?) into that work would have been a considerable difficulty. (Just consider the difficulty that would have formed in even just maintaining a special fleet of Lancasters in the US — you'd need to import not just the planes, and the mechanics, and probably the crew, but also enough infrastructure to keep them repaired and ready to go, and that would be a considerable investment of time and effort. Whereas with B-29s you would be using existing facilities very easily.) Groves later used a justification like this to talk about why the Lancaster wouldn't work. (The comments to my blog post have a lot of further back and forth over whether a Lancaster was technically viable or not — I am not a plane guy, and I think the logistical difficulties are great enough to rule it out even if it was still technical feasible, which isn't clear to me.)

• This was a later consideration, but the atomic bomb could only be safely delivered during the war if nobody knew the plane that had it was carrying an atomic bomb. (The Silverplate B-29s were in fact mostly defenseless, and had most of their defensive armament and all of their armor removed.) That only works if they don't stand out. A lone B-29, by mid-1945, would not — there were dozens of B-29s over Japan every day doing reconnaissance, making weather reports, and so on. A lone Lancaster would have stood out like a sore thumb, risking the crew. If the goal was to drop the atomic bomb on Japan, then a plane capable of blending in with others in the Pacific Theater would be necessary — and that meant the B-29. (This, incidentally, was also Groves' answer for why, even if they had had an atomic bomb in time to use in Europe, it would have been difficult to do: they would not have been able to field B-29s in Europe without them sticking out.)

Aside from the "not developed here" syndrome, the B-29 was a much more advanced bomber type than the Lancaster. The American plane was pressurized, which allowed it to have a service ceiling that was much higher than the Lancaster's (ca. 30000 ft. vs. 25000). The B-29 was also a faster aircraft with a cruise speed in the upper 200 mph range while the Lanncaster's was around 200-210 mph. Range was also important for a Pacific-based aircraft and the Lancaster's was around 1000 miles less than the Boeing plane. All of this made the B-29 more survivable and more suitable for such cutting-edge technology like atomic weapons.

It also should be stressed that the B-29 was developed concurrently with the Manhattan project. Planners in neither program knew if their program would bear fruit or not. A good many of the planners in the Boeing project were unaware of the Manhattan project and Groves delegated USN Captain William Parsons and the civilian Norman Ramsey to find a suitable aircraft for the device in 1943. After some consideration, they elected on the B-29 as the ideal choice as it was nearing operational status and Hap Arnold personally "insisted" that the B-29 be the delivery plane. Boeing could modify some planes on the assembly line for special duties, codenamed "silverplate."